J. Microbiol. Biotechnol.

(2009), 19(7), 635–646

doi: 10.4014/jmb.0803.226
First published online 23 October 2008

REVIEW

Applications of DNA Microarray in Disease Diagnostics

Yoo, Seung Min1, Jong Hyun Choi1, Sang Yup Lee1,2, and Nae Choon Yoo3*
1
Department of Chemical and Biomolecular Engineering (BK21 Program), BioProcess Engineering Research Center, Center for
Systems and Synthetic Biotechnology, and Institute for the BioCentury, KAIST, Daejeon 305-701, Korea
2
Department of Bio and Brain Engineering, and Bioinformatics Research Center, KAIST, Daejeon 305-701, Korea
3
Department of Internal Medicine, Department of Oncology and Cancer Center, Yonsei University College of Medicine, Seoul
120-752, Korea
Received: March 26, 2008 / Revised: August 28, 2008 / Accepted: September 8, 2008

Rapid and accurate diagnosis of diseases is very important probe nucleic acids with target nucleic acids from clinical
for appropriate treatment of patients. Recent advances in samples are allowing effective detection of various diseases
molecular-level interaction and detection technologies with high speed, sensitivity, and specificity. In addition, the
are upgrading the clinical diagnostics by providing new availability of the complete genome sequences of disease-
ways of diagnosis, with higher speed and accuracy. In causing organisms and of the human is changing the way
particular, DNA microarrays can be efficiently used in of designing probes for the accurate diagnosis of diseases
clinical diagnostics which span from discovery of disease- caused by them.
relevant genes to diagnosis using its biomarkers. Diagnostic A DNA microarray is generally composed of a solid support
DNA microarrays have been used for genotyping and onto which multiple DNA probes with known identities
determination of disease-relevant genes or agents causing are fixed for molecular hybridization with clinical samples
diseases, mutation analysis, screening of single nucleotide (J. P. Fruehauf et al. 2008: US7323300; M. J. Heller et al.
polymorphisms (SNPs), detection of chromosome 1998: US5849486A1; M. Chee et al. 1998: US5837832A1;
abnormalities, and global determination of posttranslational E. A. Hubbell et al. 1999: US5856101A1; M. Chee et al.
modification. The performance of DNA-microarray-based
diagnosis is continuously improving by the integration of
other tools. Thus, DNA microarrays will play a central role
in clinical diagnostics and will become a gold standard
method for disease diagnosis. In this paper, various
applications of DNA microarrays in disease diagnosis are
reviewed. Special effort was made to cover the information
disclosed in the patents so that recent trends and missing
applications can be revealed.
Keywords: DNA microarray, diagnosis, biomarker, genetic
disorder, single nucleotide polymorphism

Diagnostic assays are playing an increasingly important

role in the subsequent treatment of diseases. A rapid,
accurate, and reliable diagnostic method is very important,
as it allows identification of the disease for suitable
therapy, which consequently can reduce the mortality rate
and also the cost of treatment. The recently developed
molecular diagnostic assays based on the hybridization of
*Corresponding author
Phone: +82-11-9163-7604; Fax: +82-2-393-3652;
E-mail: ync0011@yumc.yonsei.ac.kr
Fig. 1. Use of DNA microarrays for the diagnosis of diseases.
DNA microarrays can be used for diagnosing various diseases via
genotyping and determination of genes involved in the diseases, detection
of infectious pathogens from the samples of patients, detection of
chromosome abnormalities and mutations causing genetic disorders, SNPs
screening, and global determination of posttranslational modifications
associated with diseases.
636 Yoo et al.

1999: US5861242A1; K.-K. Wong et al. 1999: US5925522A1).
It has been utilized in various fields including gene discovery,
disease diagnosis, drug discovery, and toxicological research
[26]. The DNA microarray allows more rapid, reliable,
efficient, reproducible, precise, and high-throughput detection
of diseases or disease-causing agents compared with the
other techniques used to date. Several applications of DNA
microarrays for diagnosing specific diseases have been reported
(Fig. 1): genotyping and determination of disease-relevant
genes or disease-causative agents, mutation analysis using
relatively low-density DNA microarrays, single nucleotide
polymorphisms (SNPs) screening using high-density DNA
microarrays, analysis of copy number changes at the level
of chromosome using comparative genomic hybridization
DNA microarrays (arrayCGH), and global determination
of posttranslational modifications including methylation,
acetylation, and alternative splicing.
This review focuses on the applications of DNA microarrays
for diagnosing diseases. Application of DNA microarrays for
diagnosing and studying cancer is not covered in this paper
as there are numerous papers for the readers to consult on.
As the intellectual properties can guide the direction of
new research, we reviewed the patents on the applications
of DNA microarrays for disease diagnosis (Table 1). First,

Table 1. Patents on the applications of DNA microarrays in disease diagnosis.

Target disease or
Classification Patent No.
disease-causative agent
Diagnosis using US6905827 Chronic inflammatory
disease-related diseases (especially,
biomarker systemic lupus
erythematosis)
US20040077020A1 Inflammatory bowel
disease, Crohn’s disease
and ulcerative colitis
US20070292857A1 Type 1 diabetes
Chromosome US20070048742A1 Down’s syndrome, Patau Disease-relevant
abnormalities syndrome, Edward chromosome
detection syndrome, Turner
syndrome, Klinefelter
syndrome, Alpha-
Thalassemia Retardation-
16, Charcot-Marie-Tooth
neuropathy 1A, Cri-du-
chat syndrome, hereditary
neuropathy with liability to
pressure palsies disease,
Prader-Willi syndrome,
Rubinstein-Taybi
syndrome, Williams
syndrome, and Wolf-
Hirschhorn syndrome
Target genes or
Features
regions
Whole genomic • Using genes obtained from microarray
DNAs analysis for the expression of sequences
Disease-relevant in clinical samples
gene
Acidic calponin, • Microarray analysis for the expression
Arp 2/3 protein of 2,400 sequences in peripheral blood
complex subunit 34- mononuclear cells from patient and
Arc, human antigen healthy
CD36, human • Development of diagnostic microarray
epidermal growth consisting of gene sequence obtained
factor receptor cluster analysis
substrate, mRNA for • Confirmation of the expression of
Hrs, serine threonine disease-related genes by using real-time
kinase 11, mRNA for PCR
SHPS-1
Histone H3-K4, H3- • Chromatin immunoprecipitation (ChIP) and
K9, H3-K79, H3- cDNA microarray analysis of dimethylation,
K36 trimethylation, and acetylation of target
genes in THP-1 monocytes cell
• ChIP and cDNA microarray analysis of
dimethylation of target genes in THP-1
monocytes cell under high glucose vs.
normal glucose conditions
• ChIP and cDNA microarray analysis of
dimethylation of target gene in normal
vs. patients with Type 1 diabetes
• Fabrication of microarray comprising
specific chromosome-relevant BAC clone
reconfirmed by fluorescence in situ
hybridization (FISH)
• Enable to detect the chromosome
abnormality on genome of the organism
or in intron region
• Enable to investigate the relationship
between specific disease and the detected
chromosome and detect the genomic
mutation aspect caused by endogeneous
or exogeneous factor
 DEVELOPMENT OF DIAGNOSTIC DNA MICROARRAY 637

Table 1. Continued.
Target disease or Target genes or
Classification Patent No. Features
disease-causative agent regions
Monogenic US6979542 Autosomal recessive Whole genomic • Analysis of a genetic signature for
disease-related disorders (ataxia DNAs, heterozygous carriers of autosomal recessive
mutation telangiectasia, cystic Disease-relevant disorders
detection fibrosis, sickle cell gene
anemia, Tay-Sachs disease,
Phenylketonuria,
oculocutaneuos albinism,
hereditary
hemochromatosis, AAT
deficiency, ADA
deficiency, beta-
thalassemia, alpha-1
antitrypsin deficiency,
spinal muscular atrophy,
Friedreich’s atoxia,
congenital adrenal
hyperplasia)
WO07083928A1 Corneal dystrophy βIGH3 gene • Enable to detect the mutation associated
with Avellino dystrophy (R124H), lattice
type I dystrophy (R124C), Reis-Bucklers
I (R124L), and granular type (R555W)
• Showing 100% accuracy (n=98) compared
with DNA sequencing
US20040132015A1 Genetic disorder Disease-relevant • Identification of disease-associated mutation
(e.g., Wilson disease), gene (ATP7B gene) using codon-scanning algorithm in which
single nucleotide allele-specific probes are designed by
polymorphisms (SNPs) changing three consecutive bases of
codon sequence of gene related to disease
US20030073082A1 Congenital adrenal 21-Hydroxylase gene • Immobilization of tandem cDNA fragments
hyperplasia (exon 1, intron 2, exon amplified from 7 sets of constructed vectors
4) containing target genes
SNPs US20060263815A1 Cardiovascular diseases Disease-relevant • Diagnosis of cardiovascular disease by
detection gene detecting multiple single nucleotide
polymorphisms in disease-relevant genes,
yielding the distinct patterns of genotypes
US20070196845A1 SNPs Disease-relevant • Detection of SNPs through four steps;
gene hybridization, cleavage of mismatch sites,
denaturation of hybridized dimer, and
detection of four detection probes with
dsDNA
Bacteria US20020187490A1 Pseudomonas fluorescens, Whole genomic • Detection of arrayed probes to produce a
detection P. chlororaphis, P. putida, DNAs hybridization pattern
P. aeruginosa
US20080020379A1 Mycoplasma, Bordetella Host genes expressed • Providing gene expression profiles caused
pertussis, Chlamydia specifically by by respiratory infection
pneumoniae pathogen exposure • Using gene expression markers from
blood that are indicative of host response
to exposure, response, and recovery of
pathogen infections

the development of DNA microarrays containing the
specific biomarkers for diagnosing various diseases including
metabolic, autoimmune, and inflammatory diseases is
reviewed. Then, DNA microarrays developed for the detection
of mutations associated with genetic disorders are described.
Finally, DNA microarrays developed for the detection and
identification of infectious agents are reviewed. In particular,
those for detecting pathogenic microorganisms causing
infectious diseases such as sepsis, bacteremia, and pneumonia
are reviewed in detail.
638 Yoo et al.

Table 1. Continued.
Target disease or Target genes or
Classification Patent No. Features
disease-causative agent regions
WO03095677A1 Acinetobacter baumannii, 23S rRNA, 16S-23S • Detection of 44 bacterial and 2 fungal
Klebsiella pneumoniae, ITS pathogens (Candida albicans, C. glabrata)
Peptostreptococcus using species-specific probes
anaerobius, • Using 7 bacteria universal probes that
Fusobacterium consist of sequences existing in all bacteria
necrophorum, • Validation of species- and bacterial-specific
Enterobacter cloacea, probes with 300 clinical isolates
Enterobacter aerogenes,
Streptococcus pneumoniae,
Staphylococcus aureus,
Burkholderia cepacia,
Salmonella enterica,
Escherichia coli,
Pseudomonas aeruginosa,
Legionella pneumoniae
US20030091991A1 Bacillus, Bordetella, 16S rDNA, 18S • Using DNA microarray comprising specific
Branhamella, Chlamydia, rDNA, toxin-related target gene amplicons with species-specific
Corynebacterium, gene, specific primers
Haemophilus, antigen gene,
Mycobacterium, Orientia antigenic gene,
virulence-related
gene,
US20060194223A1 Staphylococcus, Shigella, 23S rDNA • Combined with zipcode oligonucleotides
Mycobacterium, Listeria, and DNA microarray, allowing identifying
Campylobacter, the specific species
Lactococcus, Bacillus
US20050136432A1 Mycobacterium 16S rDNA, drug • Enable to discriminate mycobacterial
resistance-relevant species from other pathogens and detect
gene the resistance of antibiotics
US6924094 Mycobacterium rpoB gene • Detection of mycobacterial species (M.
avium, M. gordonae, M. chelonae, M.
kansasii, M. scrofulaceum, M. xenopi,
M. intracelluare, and M. tuberculosis)
by using species-specific probes designed
by tiling strategy for sequencing
determination, which show distinct
hybridization patterns
Viruses US6759193 Hepatitis B virus Surface antigen • Using probes detectable of the mutation
detection mutant 145 (glycine change (G→A) of amino acid 145 of
to arginine) human hepatitis B virus surface antigen
in serum samples
US20030186222A1 Enterovirus Enteroviral • Combined nucleic acid sequence-based
5'untranslated region amplification, DNA microarray technology,
(5'-UTR) and electrochemiluminescence
• Enable to detect Poliovirus (1, 2, 3),
Coxsackievirus (A9, A16, A21, A24,
B1, B3, B4, B5), Echovirus (5, 6, 11, 12,
70, 71)
US7301015 Human papillomavirus L1 region • Enable to detect 22 HPV genotypes
(HPV) including 15 high-risk types (HPV type
16, 18, 31, 33, 35, 39, 45, 51, 52, 56,
58, 59, 66, 68, 69) and 7 low-risk
types (HPV type 6, 11, 34, 40, 42, 43,
44)
• Showing 100% sensitivity (n=213) and
98% specificity compared with Hybrid
Capture II assay
 DEVELOPMENT OF DIAGNOSTIC DNA MICROARRAY 639

Table 1. Continued.
Target disease or Target genes or
Classification Patent No. Features
disease-causative agent regions
US20070248968A1 HPV L1, E6, E7 region • Enable to detect 40 HPV genotypes
including 20 high-risk (16, 18, 26, 30,
31, 33, 34, 35, 39, 45, 51, 52, 53, 56, 57,
58, 66, 67, 68, 70), 17 low-risk (6, 7, 10,
11, 27, 32, 40, 42, 44, 54, 55, 59, 61, 62,
72, 73, 83), and 3 middle-risk types (82/
MM4, 84/MM8, CP8304/8)
• Showing 100% accuracy (n=20) compared
with DNA sequencing
US20070031826A1 HPV L1 region • Enable to detect 24 HPV genotypes
including 16 high-risk (16, 18, 31, 33,
35, 39, 45, 51, 52, 53, 54, 56, 58, 59, 66,
68) and 8 low-risk (6, 11, 34, 40, 42, 43,
44, 70) types
• Showing 91.1% accuracy (n=282)
compared with DNA sequencing
US20070207456A1 HPV E1 region • Providing 66 primers covering 89 HPV
types
• Validation of HPV type-specific primers
with cervical cancer cell line (SiHa, CaSki,
C4I, ME-180, SW765), and vulvar
carcinoma samples
US20060147905A1 Orthopoxvirus crmB gene • Enable to subdivide orthopoxvirus into
five groups (Variola virus, Monkeypox
virus, Cowpox virus, Vaccinia virus,
Rabbitpox virus) by using species-specific
probes of the crmB gene that show
distinct hybridization patterns
Fungi detection US20050260584A1 Histoplasma capsulatum, ITS (internal • Using universal fungal probes, probes for
Blastomyces dermatitidis, transcribed spacers) endemic dimorphic and species-specific
Coccidioides immitis, 2 coding region probes
Paracoccidioides (5.8S-28S)
brasiliensis, Sporothrix
schenckii, Penicillium
marneffei, Cryptococcus
neoformans, Pneumocystis
carinii, Penicillium
citrinum, Penicillium
purpurogenum
US7052836 Aspergillus lavus, ITS2 coding region • Providing ITS2 region sequences of
A. fumigates, A. niger, (5.8S-28S) target fungal species (Aspergillus, Fusarium,
A. terreus, A. nidulans, Mucor, Penicillium, Rhizopus, and
Fusarium solani, F. Rhizomucor species)
moniliforme, Mucor ouxii,
M. racemosus, M.
plumbeus, M. indicus, M.
circinilloides f.
circinelloides, Rhizopus
oryzae, R. microspores, R.
circinans, R. stolonifer,
Rhizomucor pusillus,
Absidia corymbifera,
Cunninghamella elegans,
Pseudallescheria boydii,
Penicillium notatum,
Sporothrix schenkii
US7291465 Stachybotrys-chartarum, Species-specific • Using multiple pairs of primers specific
Aspergillusersicolor, A. genes for the same species of fungi
fumigates, Penicillium • Enable to detect multiple species
spinulosum, P. chrysogenum simultaneously
640 Yoo et al.
DIAGNOSTIC DNA MICROARRAY USING DISEASE-
RELEVANT BIOMARKERS
The discovery of new specific biomarkers related to a
particular disease is very important for its accurate diagnosis,
drug discovery, and toxicity test.
The conventional methods such as the hypothesis-based
approaches to biomarker discovery usually consider that
only one to several potential markers are investigated at a
time. Thus, these methods result in a relatively low rate of
successful discovery. On the other hand, the biomarker
discovery using the DNA microarray can be carried out by
analyzing global expression levels under different genotypic,
phenomic, and environmental conditions, thus allowing
global-scale candidate identification (D. D. Shoemaker et al.
2004: US6713257). It allows simultaneous identification
of candidate biomarkers by analyzing differentially expressed
genes under comparative conditions such as healthy vs.
diseased states (J. P. Fruehauf et al. 2008: US7323300; P.
Tamayo et al. 2008: US7324926; J. D. Shaughnessy et al.
2005: US20050112630A1; E. Wang, 2007: US7157227;
A. Slominski et al. 2007: US20070059711A1). By carefully
applying clinical samples at various stages or conditions to
the DNA microarray, those genes that are specifically
associated with different disease stages or conditions can
be revealed [8].
DNA microarray-based approaches for biomarker discovery
have been applied for studying several chronic diseases
including diabetes [7], arthritis [8], and cardiovascular
disease [33]. For example, biomarkers for diagnosing systemic
lupus erythematosis (SLE) and rheumatoid arthritis (RA),
which are chronic autoimmune and inflammatory disorders,
can be screened by expression profiling in leukocytes because
the differential gene expression in leukocytes is clearly
relevant to SLE and RA. Osteoarthritis, the degenerative
joint disease that can be confused with RA, can also be
diagnosed by using the expression profiling of leukocytes
[21]. Based on these facts, Wohlgemuth and coworkers (J.
Wohlgemuth et al. 2007: US6905827) developed a method
for diagnosing and monitoring an autoimmune or chronic
inflammatory disease, particularly SLE, based on the
differentially expressed genes. The selected genes were
studied further by comparing them with the clinical data.
The nucleotide sequences of the selected genes were
determined and employed for the diagnosis of these
diseases.
Crohn’s disease, ulcerative colitis, and inflammatory
bowel disease (IBD) could also be diagnosed by using
the biomarker genes selected from gene expression
profiling using DNA microarray (E. Mannick et al. 2004:
US20040077020A1). Specifically, the diagnosis of IBD
with high prevalence rate and morbidity is important for
prognosis evaluation and treatment [9, 23, 25]. Mannick
and colleagues fabricated the diagnostic chip for these
diseases based on the sequences of over- and under-expressed
genes selected from Affymetrix GeneChip experiments
(E. Mannick et al. 2004: US20040077020A1). As a result,
in IBD patients, 25 sequences were identified as IBD-
relevant genes, resulting in a sensitivity of 84% and a
specificity of 100%. In Crohn’s disease, from those with
ulcerative colitis, 36 genes were identified as Crohn’s
disease-relevant genes with ulcerative colitis, resulting in a
sensitivity of 89% and a specificity of 80%.
Natarajan and Miao developed a DNA microarray for
mapping histone modification in gene coding regions
involved in gene regulation and expression (R. Natarajan
et al. 2007: US20070292857A1). They compared the
histone modification patterns within the coding regions of
disease-specific gene(s) by genome-wide location analysis
using chromatic immunoprecipitation linked to cDNA
microarrays. Those genes showing up (over 2-fold) and
down (under 0.5-fold) expressed genes under specific
conditions were selected. This patent suggested a method
for determining a risk of developing the disease, by examining
the presence or absence of histone modification in genes
(H3-K9 dimethylation) associated with type 1 diabetes,
which is an autoimmune disorder that can be followed
by complications such as retinopathy, neuropathy, and
nephropathy.
DNA MICROARRAY FOR THE DIAGNOSIS OF
GENETIC DISORDERS
Genetic disorders are obviously caused by the inherited
genetic abnormality. Chromosome abnormality and mutations
in the DNA sequence are the two types of disorders. The
latter can cause changes in the amino acid sequence in
proteins, lack of protein production, and/or different
splicing, causing disease phenotypes. Other than these,
SNPs also turned out to be important clues for tracking
disease genes, in particular those genes causing disease
development at different stages of life.
Conventional methods for mutation detection include
gel-based sequencing of polymerase chain reaction (PCR)
amplified material, restriction fragment length polymorphism
(RFLP), and single-strand conformation polymorphism
(SSCP). These sequencing procedures, in spite of their
effectiveness, are time-consuming and laborious. To satisfy
the needs for more effective mutation screening, conformation-
sensitive gel electrophoresis (CSGE) [1, 30] and capillary
electrophoresis (CE) [4] are being extensively used to
screen large number of genes for studying sequence variations
and genetic diseases. Furthermore, DNA microarray has
been developed and applied to various diagnostic fields
including genetic counseling, and SNP screening and
typing. In practice, the improved microarray techniques
have provided much advantage to analysis of genetic

mutations and SNPs in a high-throughput manner, and thus
accumulation of large amounts of data is ongoing for their
use in disease diagnosis.
DETECTION OF CHROMOSOMAL ABNORMALITIES
Genetic disorder can be caused by a chromosome abnormality
such as deletion or duplication of a chromosome, deletion
or duplication of a part of chromosome, or a break,
translocation, or inversion in the chromosome. The diseases
caused by chromosome abnormalities include several types
such as Down’s syndrome (associated with chromosome 21),
Edwards syndrome (chromosome 18), Patau syndrome
(chromosome 13), Turner syndrome (XO), and Klinefelter
syndrome (XXY), leading to irreversible physical and
mental abnormalities and death, and even fetal death.
Kang and coworkers developed a DNA microarray for
detecting chromosomal abnormalities causing various
genetic disorders consisting of Down’s syndrome, Patau
syndrome, Edward syndrome, Turner syndrome, Klinefelter
syndrome, alpha-thalassemia retardation-16, Charcot-
Marie-Tooth neuropathy 1A, Cri-du-chat syndrome, hereditary
neuropathy with liability to pressure palsies (HNPP) disease,
Prader-Willi syndrome, Rubinstein-Taybi syndrome, Williams
syndrome, and Wolf-Hirschhorn syndrome (J.-J. Kang et al.
2007: US20070048742A1). They used the bacterial artificial
chromosome chip (BAC chip) to diagnose chromosomal
abnormalities.
DETECTION OF MUTATIONS CAUSING MONOGENIC
DISEASES
Monogenic diseases are largely divided into two types
according to etiological classification: dominant and recessive
disorders. Corneal dystrophy caused by mutation in the
gene coding for βIG-H3 is one of the autosomal dominant
diseases. It begins with a blurry symptom in the center of
the cornea and ends up with vision loss as a patient gets
older. In the case of Avellino corneal dystrophy, heterozygous
mutation causes severe loss of vision as one gets older,
whereas homozygous mutation brings out complete loss of
vision much sooner. In recent years, this disease having
1/340-1/1,000 prevalence rates in Korea (in the case of
heterozygote) is coming into the spotlight because of LASIK
surgery [2, 17, 24, 29, 42]. If a patient with heterozygous
Avellino corneal dystrophy receives LASIK surgery, the opacity
of the cornea starts to develop aggressively and eventually
results in vision loss after 2 years [27]. A group of scientists
developed a DNA microarray for the diagnosis of corneal
dystrophy by detecting the mutations in exons 4 and 12 of
the βIG-H3 (S. Y. Lee et al. 2007: WO07083928) [55].
This chip was optimized with various factors for high
DEVELOPMENT OF DIAGNOSTIC DNA MICROARRAY 641
specificity and sensitivity: the capture probe concentration
(100, 50, 30, and 10 µM), the length of capture probe
ranging from 11 to 17 mers, and hybridization time (1, 2,
3, 4, 6, and 24 h). This DNA microarray was validated for
its performance using the blood samples from 98 patients,
resulting in 100% of accuracy.
In general, heterozygous mutation does not cause a
disease. However, carriers of ataxia telangiectasia (AT),
which is a recessive disorder, show reduced life span, high
risk for cancer (especially breast cancer), and elevated
sensitivity to ionizing irradiation [6, 44, 45]. Unfortunately,
the AT-relevant gene is large (about 150 kb) and has
no common mutations, so it is difficult to diagnose AT
[10, 14, 20, 54]. Thus, to identify heterozygous carriers of
autosomal recessive disorders, Cheung et al. invented a cDNA
microarray that exhibits different genetic signatures from the
heterozygous mutation carriers and normal individuals
(V. G. Cheung et al. 2005: US6979542). Wilson disease
(WD) also has a similar problem of the difficulties in
searching and detecting mutations in the WD-relevant gene
(ATP7B) spanning more than 80 kb. Thus, the development
of a more efficient method for detecting WD mutations has
been in urgent need [19, 38, 39, 46, 47, 49]. Lee et al. (S. Y.
Lee et al. 2004: US20040132015A1) developed a diagnostic
DNA microarray for detecting the mutations causing WD
by using a codon scanning algorithm (COSA), which
facilitates an oligonucleotide probe design. COSA is a
probe design method in which allele-specific probes are
designed by changing three consecutive bases in the codon
sequence of the gene related to the disease. Using this
method, a DNA microarray was fabricated to cover all
reported 16 substitution mutations causing WD. It was used
to successfully diagnose nine WD patients, while distinguishing
three normal persons.
In another report, a diagnostic kit for congenital adrenal
hyperplasia (CAH) was developed by Jin (D. K. Jin.
2003: US20030073082A1). In humans, CAH is one of
the most common innate defects of metabolism (cortisol
biosynthesis) and observed in a rather high frequency of 1
in 10,000. As infants with CAH suffer from the loss of
salts, hyperkalemic acidosis and dehydration occur and
infants can finally die unless treated with steroid hormone
replacement. Thus, early diagnosis is critical [35, 41, 53].
Jin employed 7 sets of tandem cDNA fragments of normal
and patient’s 21-hydroxylase gene (exon 1, intron 2, and
exon 4) for detecting point mutations in this gene (D. K.
Jin. 2003: US20030073082A1).
Detection of Polymorphic Changes
Polymorphic changes (so-called SNPs) are genetic variations
occurring at a frequency of about one in every 1,000 bases
in the genome. The SNPs can exhibit an individual’s
susceptibility to a particular disease. Recently, much effort
has been made to find disease-relevant markers using an SNP
642 Yoo et al.
microarray, so-called multi-SNP markers (S.-H. Choi et al.
2006: US20060263815A1). High-throughput screening of
SNPs using DNA microarrays may make it possible to
predict responses to a specific medicine and disease diagnosis,
leading to its ultimate use towards developing personalized
medicine. However, the lack of a suitable discriminative
power in detecting one base difference using DNA microarrays
makes its use as a detection tool difficult. Negishi tried
to enhance the detection accuracy of the DNA chip by
removing the unhybridized probes (M. Negishi. 2007: US
20070196845A1). Probes immobilized on the slide were
designed with a flanking sequence around SNPs and
different bases at SNP sites. These probes were hybridized
with target DNAs having the flanking sequence around the
SNPs in the gene. Unhybridized probes (three of four
probes) were cleaved off by the single-stranded DNA
(ssDNA)-cleaving enzyme and denatured in ssDNA form.
This invention enhanced the discriminative power of the
DNA microarray for SNPs detection employing specific
strand cleaving enzymes, and thus is suitable for high-
throughput screening of SNPs with high accuracy.
DNA MICROARRAY FOR THE DIAGNOSIS OF
INFECTIOUS DISEASES
Human beings have been continuously fighting with
pathogens causing infectious diseases. Infectious diseases
have been a major cause of deaths in the 20the century and
is still so [36]. Recently, the emergence of infectious diseases
has become more serious, as represented by new pathogens
such as the viruses causing acquired immune deficiency
syndrome (AIDS), Nipah virus encephalitis, avian influenza,
dengue fever, and West Nile encephalitis; re-emerging
pathogens such as those causing malaria, measles, foodborne
pathogens; and antibiotic-resistant superbacteria such as
methicillin-resistant Staphylococcus aureus, vancomycin-
resistant S. aureus, and multidrug-resistant Mycobacterium
tuberculosis [36]. To make the situation worse, it has
become more difficult to diagnose and treat these infectious
diseases because of the abuse of antibiotics, overuse of
immunosuppressants in transplantation, and overdose of
drugs as anticancer therapy. Rapid detection and accurate
identification of pathogenic agents are critical to treating the
patients with appropriate therapeutic agents. Various methods
have been developed and used for the detection and
identification of pathogenic microbes. Several techniques
such as culture-based, serological [40], and immunological
[37] assays have been developed, and remarkable progress
has been made in the area of nucleic acid-based assays (e.g.,
PCR-based assays [31]). However, the culture-based assay,
which is an automatic system coupled with biochemical
test for the identification of microbial pathogens, has a low
success rate especially when antibiotics are administrated
to patients. Serological and immunological methods often
generate nonspecific adsorption, resulting in high false-
positive values, poor reproducibility, low speed, and intensive
labor. On the other hand, recent advances in DNA microarray
analysis have revolutionized molecular approaches towards
detection of microbial pathogens by not only enhancing
assay capabilities (sensitivity and specificity), but also
allowing high-throughput detection. Most of all, the
compatibility of DNA microarray with miniaturized devices
can result in enhanced speed, sensitivity, and portability,
which are important factors in the field of diagnostics.
Detection of Pathogenic Bacteria
There have been several reports on the development
of microarrays for the detection of bacteria (J. Tiedje
et al. 2002: US20020187490A1; B. K. Agan et al.
2008: US20080020379A1; B. K. Agan et al. 2006:
US20060210967A1). Anthony and colleagues [5] developed
a microarray for the identification of bacteria by using
universal PCR primers capable of amplifying bacterial 23S
rRNA. They evaluated the microarray with blood cultured
samples from bacteremia patients. Wang and coworkers
[50, 51] developed a 16S rRNA-based microarray for the
detection of intestinal bacteria in fecal samples. The
predominant bacterial species in the human fecal samples
are anaerobic bacteria that often require at least a 5-day-long
culture for their detection. In this study, 20 predominant
human intestinal bacterial species from fecal samples were
directly detected by microarray-based assay. However, in
contrast with the cases of using sterile specimens such as
blood, the existence of other bacteria in nonsterile specimens
such as feces makes it difficult to accurately identify the
diseases-causing pathogens. On the other hand, Cleven
et al. [12] detected bacteremia-causing bacterial species
such as S. aureus, E. coli, and Pseudomonas aeruginosa
by employing bacterial species-specific genes, including
housekeeping genes, virulence factors, and antibiotic resistance
determinants, instead of ribosomal RNA sequences. Here, the
gene-specific PCR products were immobilized on the slide
glass as capture probes and subsequently used for the
characterization of the bacteria in terms of antibiotics
resistance and virulence. Recently, Lee and his colleagues
reported design strategies and probe sequences for the detection
of 44 pathogenic bacteria, which were selected based on
their high prevalence in infectious states and/or difficulty
of cultivation (S. Y. Lee et al. 2003: WO03095677A1). The
thus-developed DNA microarray, named PathoChipTM, was
evaluated by applying a variety of clinical isolates from
blood, sputum, stool, cerebral spinal fluid, pus, and urine.
Based on the 23S rDNA and 16S-23S rDNA ISR sequence
analysis, the bacteria- and bacterial species-specific probes
were designed by considering relations between the probe
properties and hybridization efficiency. Specific nucleotide
sequences solely present in the microbe of interest were

identified by performing multiple alignment of nucleotide
sequences derived from all microorganism species. The
specificity and sensitivity of the candidate probes were first
confirmed by comparison with the sequences in public
databases by BLAST analyses and then reconfirmed by
hybridization studies with clinical samples. Adding bacteria-
specific probes as well as species-specific probes to this
system enabled detection of all bacteria. The selected
probes provided relatively high sensitivity and specificity
in microarray-based assay with reference bacteria and clinical
isolates from various specimens. Takayuki reported the DNA
microarray composed of DNAs amplified with 35 kinds of
primers for detecting pathogens causing respiratory infectious
disease (T. Ezaki. 2003: US20030091991A1). Thirty-five
kinds of primers were used to amplify 16S-18S sequences,
specific antigen, toxin, and virulent genes of pathogens.
Detection of pathogens in food samples was also carried out
by using DNA microarrays. Andreoli and colleagues reported
the method for identifying the contaminating microorganisms
in large amounts of foodstuff (P. Andreoli et al. 2006:
US20060194223A1). This method employed unique and
distinct oligonucleotides (ZIP-code) in manufacturing a
DNA microarray to overcome the disadvantages of whole-
genome DNA-DNA hybridization. This diagnostic microarray
was also combined with a ligase detection reaction (LDR),
which is suitable for identifying SNPs and point mutations,
as well as pathogen detection because of its powerful
discriminatory power of DNA bases.
Among many bacterial species, mycobacteria have been
receiving particular attention as this bacterium is the
world’s most notorious infectious killer, causing tuberculosis.
Although mycobacterial vaccines are available, it is still
prevalent in the undeveloped countries. According to the
report of the Center for Disease Control, mycobacterial
disease has more than 15 thousand new cases (about 70%
of the total announced number of infectious diseases) and
15 hundred deaths (five times that of the other infectious
diseases) annually. The microarray for the detection of
mycobacteria has been developed by several researchers
(K.-S. Lu et al. 2005: US20050136432A1; T. R. Gingeras
et al. 2005: US6924094). In addition, considering the
importance of drug resistance of Mycobacterium as a
serious problem encountered in the clinical treatment of
the disease, probes for detecting drug resistance have also
been reported (K.-S. Lu et al. 2005: US20050136432A1).
Detection of Pathogenic Viruses
A virus is a small infectious agent, much smaller than a
fungus or bacterium, and must invade a living cell to
replicate. Viral infection causes various symptoms such as
sore throat, sinusitis, and common cold. Viral infection can
be dangerous to the community owing to fast contagiousness.
Thus, accurate and rapid detection is crucial for the
protection against viral diseases. Viruses generally contain
DEVELOPMENT OF DIAGNOSTIC DNA MICROARRAY 643
specific nucleic acid sequences that are different by more
than 30% in the same species or even serotypes. Therefore,
it is not too difficult to detect them by nucleic acid-based
assays such as the microarray-based assay.
Hepatitis virus is responsible for chronic liver disease,
cirrhosis, and hepatocellular carcinoma. It can be detected
from a patient’s serum through various techniques such as
quantitative microarray and microarray employing nanogold-
silver stain [28, 32]. The use of gold nanoparticles treated
with silver (AgNO3) for signal amplification allowed
enhanced sensitivity, which consequently contributed to
lowering the detection limit of the assay up to 100 fM of
amplicon, corresponding to 1 copy of virus per liter of
serum. Oon and colleagues used DNA probes for detecting
human hepatitis B virus surface antigen mutant 145
(glycine to arginine) in serum samples and developed a
DNA microarray using its unique sequence (C.-J. Oon et
al. 2004: US6759193).
Enterovirus is one of the most common viral infectious
agents in humans, causing an estimated 10-15 million
infections a year in the United States [43]. A majority of
enteroviral infections result in mild illness; however,
enteroviruses can cause different diseases affecting many
organs. For example, neurologic (polio, aseptic meningitis,
encephalitis), respiratory (common cold, tonsillitis, pharyngitis,
rhinitis), and cardiovascular (myocarditis, pericarditis)
diseases can be caused by enteroviral infection. Detection
of enteroviruses has several problems: misdiagnosis confused
by bacterial or herpes virus infections in enteroviral
meningitidis, and a high degree of serological cross-reactivity
amongst the more than 70 known enteroviruses. Therefore,
the development of a system for the accurate and rapid
detection of enteroviruses is very important and urgent to
the health and welfare of those with increased potential
of exposure. Paul reported a technology for alternate
amplification and detection of enteroviruses (J. H. Paul III.
2003: US20030186222A1). Target DNAs were prepared
by nucleic acid sequence based amplification (NASBA).
NASBA is started by attaching a primer containing a T7
RNA polymerase promoter at the 3' end of mRNA. Reverse
transcriptase generates a RNA/DNA hybrid and then the
RNA of the hybrid is specifically cleaved by RNAse H. T7
RNA polymerase recognizes the T7 RNA polymerase
promoter, producing an antisense RNA product. Then,
DNA/RNA hybrid synthesis by reverse transcriptase, RNA
degradation from the RNA/DNA hybrid, duplex DNA
generation, and cycling of antisense RNA are performed.
Target DNAs amplified by NASBA are hybridized with
enteroviral-specific probes on a microarray, and viral presence
is detected by electrochemiluminescence.
Human papilloma virus (HPV), having more than 120
different types, is also an important pathogenic virus, which
infects through the skin and mucous membranes. HPV is
considered to be an etiological agent of invasive cervical
644 Yoo et al.
cancer, which represents 450,000 new cases worldwide
annually. Over 70 genotypes of HPV have been identified
since the recognition of HPV as the main etiological factor
for cervical cancer [11]. Several researchers have reported
specific probes for HPV detection (R. C. McGlennen
et al. 2007: US20070238100A1; U. Gyllensten et al.
2007: US20070037137A1; S. A. Norman et al. 2006:
US20060121516A1; S.-W. Yoon et al. 2007: US7301015;
L.-J. Van Doorn et al. 2003: US20030165821A1; M. A.
Cohenford et al. 2003: US20030108866A1; C. Wheeler et
al. 2003: US20030059806A1; P. E. Kroeger et al. 2002:
US20020137021A1; C. Jeney et al. 2007: US7294488).
Moreover, several companies have developed DNA
microarrays for HPV detection. Yoon and colleagues
developed a HPV detection chip composed of probes for
prevalent HPV types including 15 high-risk types (HPV
types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68,
and 69) and 7 low-risk types (HPV types 6, 11, 34, 40, 42,
43, and 44) (S.-W. Yoon et al. 2007: US7301015). This
chip showed 100% relative sensitivity and 98% relative
specificity compared with the conventional assay. Moon and
colleagues also developed a DNA chip containing the
probes for analyzing 40 types of HPV (W.-C. Moon et al.
2005: US20070248968A1). The probes were designed on
the basis of the sequences of L1, E6, and E7 genes of 35
types of HPV obtained from cervical cell specimens of
4,898 Korean adult women and tissue specimens of 68
cervical cancer cases, in addition to information based on
American and European cases. This chip allowed genotyping
of HPV with high sensitivity and specificity of up to
100%. Lee and colleagues developed a similar DNA chip,
allowing genotyping of 24 HPVs (D.-J. Lee et al. 2007:
US20070031826A1). Pourmand and colleagues developed
a diagnostic DNA microarray for distinguishing 89 genotypes
of HPV (N. Pourmand et al. 2007: US20070207456A1).
In another study, Ezaki introduced 12 kinds of primers
for detecting viruses causing respiratory infectious diseases,
by using the information on specific antigen, capsid, and
virulence factors (T. Ezaki, 2003: US20030091991A1).
The specific primer sets for detecting 64 strains of RNA
virus, 16 strains of DNA virus, and 15 species of Salmonella
belonging to the group E were also disclosed. Mirzabekov
developed a DNA microarray for diagnosing orthopoxvirus
(A. D. Mirzabekov et al. 2006: US20060147905A1).
Detection of Pathogenic Fungi
The infectious diseases caused by pathogenic fungi have
been increasing because of the increase of chemotherapy for
hematological malignancies, high-dose corticosteroid treatment
for organ transplant recipients, and the spread of AIDS
over the past decade [3, 34]. For example, Penicillium
marneffei is the third most common cause of opportunistic
infections in patients with AIDS in Thailand [48]. Additionally,
P. chrysogenum and P. citrinum have been well recognized as
the cause of human disease. Infection by Aspergillus, Rhizopus,
and Mucor species can be fatal in immunocompromised
patients [52]. Specifically, aspergillosis has a high mortality
rate of up to 90% [16,18].
Fungi can be diagnosed by cultivation, serological, and
histopathological assays [22]. However, these conventional
methods for detecting pathogenic fungi may require several
weeks, owing to slow growth. Specifically, in the case of
immunosuppressed patients, it is very difficult to detect
circulating antifungal antibodies in blood by serological
tests. Although the histopathological test is relatively rapid
and available to diagnosis of invasive fungal disease,
atypical morphological features cause problems in accurate
identification (M. D. Lindsley et al. 2005: US20050260584A1).
Most of the diagnostic tests are directed to genus- and
species-specific or single-copy genes. Several groups
introduced the broad-spectrum detection system with
probes designed from internal transcribed spacer (ITS)
regions of the rRNA genes. Lindsley et al. (M. D. Lindsley
et al. 2005: US20050260584A1) suggested the methods of
detecting a dimorphic fungus, including differentiating a
dimorphic fungus from other fungi. They identified the
presence or absence of fungi in blind samples by using a
dimorphic fungal probe, species-specific probe, microbe-
specific probe, and a nucleic acid sequence corresponding
to the ITS region of fungal rDNA.
Morrison and colleagues reported oligonucleotide
probes for detecting Aspergillus species and other filamentous
fungi (C. J. Morrison et al. 2006: US7052836). The unique
ITS regions allowed design of specific nucleic acid probes
for five Aspergillus, three Fusarium, four Mucor, two
Penicillium, five Rhizopus, one Rhizomucor species, Absidia
corymbifera, Cunninghamella elegans, Pseudallescheria
boydii, and Sporothrix schenkii. They also suggested
the genus-specific probes for Aspergillus, Fusarium, and
Mucor.
In another study, α-aminoapidate reductase, which is a
highly conserved protein in fungi, was employed as a
target gene for designing probes (D. K. R. Karaolis, 2007:
US7291465). This allowed enhanced detection sensitivity
and specificity. They designed the nucleic acid hybridization
probes for Candida albicans causing candidosis, a common
nosocomial infection seriously causing problems to both
immunosuppressed and postoperative patients.
FUTURE PROSPECTS
During the past two decades, DNA microarray-based
techniques have been predominantly applied to identification
of biomarkers, detection of pathogens, and identification
of disease-causative agents. In many cases, they allowed
accurate and rapid results, but their wide-spread use has
been hampered for the limited identification capability. To

increase its practical usage in diagnosis, it should become
more affordable, convenient to practice, accurate, and maybe
portable. One example is on-site pathogen and SNPs
detection (C.-B. Chae et al. 2008: US20080008990A1),
such as lateral flow assays (W. Gumbrecht et al. 2007:
US20070264630A1) that can simply and rapidly detect
pathogens and SNPs. This will enable sensitive on-site
diagnosis of specific diseases in clinical or environmental
samples. Another interesting alternative of microarrays in
medical diagnostics is the lab-on-a-chip type system,
which integrates several processes (from DNA extraction
to DNA analysis) within a single, portable, small, and
fully automated instrument (S.-H. Paek et al. 2008:
US20080019866A1). Additionally, DNA microarray systems
may be combined with other techniques such as CpG
island detection or chromatin immunoprecipitation [13,
15]. Indeed, much progress is being made on the use of the
DNA microarray platform for disease diagnosis. For the
successful diagnosis of diseases, it is of utmost importance
to have specific probes, which can be considered as the
contents of chips! Genome projects on many infectious
organisms are generating unprecedentedly large amounts of
sequence information, which can be used to design more
specific probes for the diagnosis of more diverse infectious
agents. With all these advances, it is expected that the DNA
microarray or its sister technologies will play an increasingly
important role in disease diagnosis in the near future.
Acknowledgments
Our work described in this review paper was supported by
Medigenes Co. The work at KAIST has also been partially
supported by the Korean Systems Biology Research
Project from the Ministry of Education, Science and
Technology, and LG Chem Chair Professorship.
REFERENCES
1. Acquila, M., F. Bottini, A. Valetto, D. Caprino, P. G. Mori, and
M. P. Bicocchi. 2001. A new strategy for prenatal diagnosis in a
sporadic haemophilia B family. Haemophilia 7: 416-418.
2. Afshari, N., J. Mullaly, M. Afshari, R. F. Steinert, A. P. Adamis, D.
Azar, and J. Talamo. 2001. Survey of patients with granular, lattice,
Avellino, and Reis-Bucklers corneal dystrophies for mutations in
the BIGH3 and gelsolin genes. Arch. Ophthalmol. 119: 16-22.
3. Ampel, N. M., D. G. Mosley, B. England, P. D. Vertz, K.
Komatsu, and R. A. Hajjeh. 1998. Coccidioidomycosis in
Arizona: Increase in incidence from 1990 to 1995. Clin. Infect.
Dis. 27: 1528-1530.
4. Andersen, P. S., C. Jespersgaard, J. Vuust, M. Christiansen,
and L. A. Larsen. 2003. Capillary electrophoresis-based single
strand DNA conformation analysis in high-throughput mutation
screening. Hum. Mutat. 21: 455-465.
DEVELOPMENT OF DIAGNOSTIC DNA MICROARRAY 645
5. Anthony, R. M., T. J. Brown, and G. L. French. 2000. Rapid
diagnosis of bacteremia by universal amplification of 23S
ribosomal DNA followed by hybridization to an oligonucleotide
array. J. Clin. Microbiol. 38: 781-788.
6. Athma, P., R. Rappaport, and M. Swift. 1996. Molecular genotyping
shows that ataxia telangiectasia heterozygotes are predisposed to
breast cancer. Cancer Genet. Cytogenet. 92: 130-134.
7. Baelde, H. J., M. Eikmans, P. P. Doran, D. W. Lappin, E. de
Heer, and J. A. Bruijn. 2004. Gene expression profiling in
glomeruli from human kidneys with diabetic nephropathy. Am.
J. Kidney Dis. 43: 636-650.
8. Barnes, M. G., B. J. Aronow, L. K. Luyrink, M. B. Moroldo, P.
Pavlidis, M. H. Passo, et al. 2004. Gene expression in juvenile
arthritis and spondyloarthropathy: Pro-angiogenic ELR+ chemokine
genes relate to course of arthritis. Rheumatology 43: 973-979.
9. Becker, K. G., R. M. Simon, J. E. Bailey-Wilson, B. Freidlin,
W. E. Biddison, H. F. McFarland, and J. M. Trent. 1998.
Clustering of non-major histocompatibility complex susceptibility
candidate loci in human autoimmune diseases. Proc. Natl. Acad.
Sci. USA 95: 9979-9984.
10. Broeks, A., J. H. Urbanus, A. N. Floore, E. C. Dahler, J. G.
Klijn, E. J. Rutgers, et al. 2000. ATM-heterozygous germline
mutations contribute to breast cancer-susceptibility. Am. J. Hum.
Genet. 66: 494-500.
11. Chen, S. L., C. P. Han, Y. P. Tsao, J. W. Lee, and C. S. Yin.
2006. Identification and typing of human papillomavirus in
cervical cancers in Taiwan. Cancer 72: 1939-1945.
12. Cleven, B. E., M. Palka-Santini, J. Gielen, S. Meembor, M.
Krönke, and O. Krut. 2006. Identification and characterization
of bacterial pathogens causing bloodstream infections by DNA
microarray. J. Clin. Microbiol. 44: 2389-2397.
13. Collas, P. and J. A. Dahl. 2008. Chop it, ChIP it, check it: The
current status of chromatin immunoprecipitation. Front. Biosci.
13: 929-943.
14. Concannon, P. and R. A. Gatti. 1997. Diversity of ATM gene
mutations detected in patients with ataxia-telangiectasia. Hum.
Mutat. 10: 100-107.
15. Delgado, I. J., D. S. Kim, K. N. Thatcher, J. M. LaSalle, and
I. B. Van den Veyver. 2006. Expression profiling of clonal
lymphocyte cell cultures from Rett syndrome patients. BMC
Med. Genet. 7: 61.
16. Denning, D. W. 1996. Diagnosis and management of invasive
aspergillosis. Curr. Clin. Top. Infect. Dis. 16: 277-299.
17. Dolmetsch, A. M., F. A. Stockl, R. Folberg, I. Gensini, and
M. N. Burnier Jr. 1996. Combined granular lattice dystrophy
(Avellino) in a patient with no known Italian ancestry. Can. J.
Ophthalmol. 31: 29-31.
18. Fridkin, S. K. and W. R. Jarvis. 1996. Epidemiology of nosocomial
fungal infections. Clin. Microbiol. Rev. 9: 499- 511.
19. Forbes, J. R. and D. W. Cox. 1998. Functional characterization
of missense mutations in ATP7B: Wilson disease mutation or
normal variant? Am. J. Hum. Genet. 63: 1663-1674.
20. Gilad, S., A. Bar-Shira, R. Harnik, D. Shkedy, Y. Ziv, R.
Khosravi, et al. 1996. Ataxia-telangiectasia: Founder effect
among North African Jews. Hum. Mol. Genet. 5: 2033-2037.
21. Gladkevich, A., S. A. Nelemans, H. F. Kauffman, and J. Korf.
2005. Microarray profiling of lymphocytes in internal diseases
with an altered immune response: Potential and methodology.
Mediators Inflamm. 2005: 317-330.
646 Yoo et al.
22. Hamilton, A. J. 1998. Serodiagnosis of histoplasmosis,
paracoccidioidomycosis and penicilliosis marneffei; current status
and future trends. Med. Mycol. 36: 351-364.
23. Hampe, J., S. Schreiber, S. H. Shaw, K. F. Lau, S. Bridger,
A. J. Macpherson, et al. 1999. A genomewide analysis provides
evidence for novel linkages in inflammatory bowel disease
in a large European cohort. Am. J. Hum. Genet. 64: 808-816.
24. Holland, E. J., S. M. Daya, E. M. Stone, R. Folberg, A. A.
Dobler, J. D. Cameron, and D. J. Doughman. 1992. Avellino
corneal dystrophy: Clinical manifestations and natural history.
Ophthalmology 99: 1564-1568.
25. Hugot, J. P. and G. Thomas. 1998. Genome-wide scanning in
inflammatory bowel diseases. Dig. Dis. 16: 364-369.
26. Iida, K. and I. Nishimura. 2002. Gene expression profiling by DNA
microarray technology. Crit. Rev. Oral Biol. Med. 13: 35-50.
27. Jun, R. M., H. W. Tchah, T. I. Kim, D. R. Stulting, S. E. Jung,
K. Y. Seo, D. H. Lee, and E. K. Kim. 2004. Avellino corneal
dystrophy after LASIK. Ophthalmology 111: 463-468.
28. Kawaguchi, K., S. Kaneko, M. Honda, F. H. Kawai, S. Yukihiro,
and K. Kenichi. 2003. Detection of hepatitis B virus DNA in sera
from patients with chronic hepatitis B virus infection by DNA
microarray method. J. Clin. Microbiol. 41: 1701-1704.
29. Kennedy, S. M., M. McNamara, M. Hillery, C. Hurley, L. M.
Collum, and S. Giles. 1996. Combined granular lattice dystrophy
(Avellino corneal dystrophy). Br J Ophthalmol. 80: 489-490.
30. Korkko, J., I. Kaitila, L. Lonnqvist, L. Peltonen, and L.
Ala-Kokko. 2002. Sensitivity of conformation sensitive gel
electrophoresis in detecting mutations in Marfan syndrome and
related conditions. J. Med. Genet. 30: 34-41.
31. Kotilainen, P., J. Jalava, O. Meurman, O. P. Lehtonen, E. Rintala,
O. P. Seppälä, E. Eerola, and S. Nikkari. 1998. Diagnosis of
meningococcal meningitis by broad-range bacterial PCR with
cerebrospinal fluid. J. Clin. Microbiol. 36: 2205-2209.
32. Liu, H. H., X. Cao, Y. Yang, M. G. Liu, and Y. F. Wang. 2006.
Array-based nano-amplification technique was applied in detection
of hepatitis E virus. J. Biochem. Mol. Biol. 39: 247-252.
33. Ma, J. and C. C. Liew. 2003. Gene profiling identifies secreted
protein transcripts from peripheral blood cells in coronary artery
disease. J. Mol. Cell. Cardiol. 35: 993-998.
34. McNeil, M. M., S. L. Nash, R. A. Hajjeh, M. A. Phelan, L. A.
Conn, B. D. Plikaytis, and D. W. Warnock. 2001. Trends in
mortality due to invasive mycotic diseases in the United States,
1980-1997. Clin. Infect. Dis. 33: 641-647.
35. Morel, Y. and W. L. Miller. 1991. Clinical and molecular
genetics of congenital adrenal hyperplasia due to 21-hydroxylase
deficiency. Adv. Hum. Genet. 20: 1-68.
36. Morens, D. M., G. K. Folkers, and A. S. Fauci. 2004. The
challenge of emerging and re-emerging infectious diseases.
Nature 430: 242-249.
37. Mulligan, M. E., L. R. Peterson, R. Y. Kwok, C. R. Clabots,
and D. N. Gerding. 1988. Immunoblots and plasmid fingerprints
compared with serotyping and polyacrylamide gel electrophoresis
for typing Clostridium difficile. J. Clin. Microbiol. 26: 41-46.
38. Payne, A. S., E. J. Kelly, and J. D. Gitlin. 1998. Functional
expression of the Wilson disease protein reveals mislocalization
and impaired copper-dependent trafficking of the common H1069Q
mutation. Proc. Natl. Acad. Sci. USA 95: 10854-10859.
39. Petrukhin, K., S. Lutsenko, I. Chernov, B. M. Ross, J. H.
Kaplan, and T. C. Gilliam. 1994. Characterization of the Wilson
disease gene encoding a P-type copper transporting ATPase:
Genomic organization, alternative splicing, and structure/function
predictions. Hum. Mol. Genet. 3: 1647-1656.
40. Rennie, R. P., C. E. Nord, L. Sjoberg, and I. B. R. Duncan.
1978. Comparison of bacteriophage typing, serotyping, and
biotyping as aids in epidemiologic surveillance of Klebsiella
infections. J. Clin. Microbiol. 8: 638-642.
41. Speiser, P. W., B. Dupont, P. Rubinstein, A. Piazza, A. Kastelan,
and M. I. New. 1985. High frequency of nonclassical steroid
21-hydroxylase deficiency. Am. J. Hum. Genet. 37: 650-667.
42. Stewart, H. S., A. E. Ridgway, M. J. Dixon, R. Bonshek, R.
Parveen, and G. Black. 1999. Heterogeneity in granular corneal
dystrophy: Identification of three causative mutations in the
TGFBI (BIGH3) gene - lessons for corneal amyloidogenesis.
Hum. Mutat. 14: 126-132.
43. Strikas, R. A., L. Anderson, and R. A. Parker. 1986. Temporal
and geographic patterns of isolates of nonpolio enteroviruses in
the United States, 1970-1983. J. Infect. Dis. 153: 346-351.
44. Swift, M., D. Morrell, E. Cromartie, A. R. Chamberlin, M. H.
Skolnick, and D. T. Bishop. 1986. The incidence and gene
frequency of ataxia-telangiectasia in the United States. Am. J.
Hum. Genet. 39: 573-583.
45. Swift, M., D. Morrell, R. B. Massey, and C. L. Chase. 1991.
Incidence of cancer in 161 families affected by ataxia-
telangiectasia. N. Engl. J. Med. 325: 1831-1836.
46. Thomas, G. R., O. Jensson, G. Gudmundsson, L. Thorsteinsson,
and D. W. Cox. 1995. Wilson disease in Iceland: A clinical and
genetic study. Am. J. Hum. Genet. 56: 1140-1146.
47. Thomas, G. R., P. C. Bull, E. A. Roberts, J. M. Walshe, and
D. W. Cox. 1994. Haplotype studies in Wilson disease. Am. J.
Hum. Genet. 54: 71-78.
48. Vanittanakom, N. and T. Sirisanthana. 1997. Penicillium marneffei
infection in patients infected with human immunodeficiency
virus. Curr. Top. Med. Mycol. 8: 35-42.
49. Waldenstrom, E., A. Lagerkvist, T. Dahlman, K. Westermark, and
U. Landegren. 1996. Efficient detection of mutations in Wilson
disease by manifold sequencing. Genomics 37: 303-309.
50. Wang, R. F., M. L. Beggs, L. H. Robertson, and C. E.
Cerniglia. 2002. Design and evaluation of oligonucleotide-
microarray method for the detection of human intestinal bacteria
in fecal samples. FEMS Microbiol. Lett. 213: 175-182.
51. Wang, R. F., S. J. Kim, L. H. Robertson, and C. E. Cerniglia.
2002. Development of a membrane-array method for the
detection of human intestinal bacteria in fecal samples. Mol.
Cell. Probes. 16: 341-350.
52. Warnock, D. W. 1995. Fungal complications of transplantation:
Diagnosis, treatment, and prevention. J. Antimicrob. Chemother.
36(Suppl B): 73-90.
53. White, P. C., M. I. New, and B. Dupont. 1987. Congenital
adrenal hyperplasia. N. Engl. J. Med. 316: 1519-1524.
54. Wright, J., S. Teraoka, A. Onengut, S. A. Tolun, R. A. Gatti,
H. D. Ochs, and P. Concannon. 1996. A high frequency of
distinct ATM gene mutations in ataxia-telangiectasia. Am. J.
Hum. Genet. 59: 839-846.
55. Yoo, S. Y., T.-I. Kim, S. Y. Lee, E. K. Kim, K. C. Keum, N. C.
Yoo, and W. M. Yoo. 2007. Development of DNA chip for the
diagnosis of most common corneal dystrophies caused by mutations
in the betaigh3 gene. Br. J. Opththalmol. 91: 722-727.